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DiCandia MA, Edwards AN, Alcaraz YB, Monteiro MP, Lee CD, Vargas Cuebas G, Bagchi P, McBride SM. A conserved switch controls virulence, sporulation, and motility in C. difficile. PLoS Pathog 2024; 20:e1012224. [PMID: 38739653 PMCID: PMC11115286 DOI: 10.1371/journal.ppat.1012224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 05/23/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024] Open
Abstract
Spore formation is required for environmental survival and transmission of the human enteropathogenic Clostridioides difficile. In all bacterial spore formers, sporulation is regulated through activation of the master response regulator, Spo0A. However, the factors and mechanisms that directly regulate C. difficile Spo0A activity are not defined. In the well-studied Bacillus species, Spo0A is directly inactivated by Spo0E, a small phosphatase. To understand Spo0E function in C. difficile, we created a null mutation of the spo0E ortholog and assessed sporulation and physiology. The spo0E mutant produced significantly more spores, demonstrating Spo0E represses C. difficile sporulation. Unexpectedly, the spo0E mutant also exhibited increased motility and toxin production, and enhanced virulence in animal infections. We uncovered that Spo0E interacts with both Spo0A and the toxin and motility regulator, RstA. Direct interactions between Spo0A, Spo0E, and RstA constitute a previously unknown molecular switch that coordinates sporulation with motility and toxin production. Reinvestigation of Spo0E function in B. subtilis revealed that Spo0E induced motility, demonstrating Spo0E regulation of motility and sporulation among divergent species. Further, 3D structural analyses of Spo0E revealed specific and exclusive interactions between Spo0E and binding partners in C. difficile and B. subtilis that provide insight into the conservation of this regulatory mechanism among different species.
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Affiliation(s)
- Michael A. DiCandia
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Ysabella B. Alcaraz
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Marcos P. Monteiro
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Cheyenne D. Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Germán Vargas Cuebas
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
| | - Pritha Bagchi
- Emory Integrated Proteomics Core, Emory University, Atlanta, Georgia, United States of America
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
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Lee CD, Rizvi A, McBride SM. KipOTIA detoxifies 5-oxoproline and promotes the growth of Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592088. [PMID: 38746432 PMCID: PMC11092664 DOI: 10.1101/2024.05.01.592088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Clostridioides difficile is an anaerobic enteric pathogen that disseminates in the environment as a dormant spore. For C. difficile and other sporulating bacteria, the initiation of sporulation is a regulated process that prevents spore formation under favorable growth conditions. In Bacillus subtilis , one such mechanism for preventing sporulation is the Kinase Inhibitory Protein, KipI, which impedes activation of the main sporulation kinase. In addition, KipI functions as part of a complex that detoxifies the intermediate metabolite, 5-oxoproline (OP), a harmful by-product of glutamic acid. In this study, we investigate the orthologous Kip proteins in C. difficile to determine their roles in the regulation of sporulation and metabolism. Using deletion mutants in kipIA and the full kipOTIA operon, we show that unlike in B. subtilis, the Kip proteins have no significant impact on sporulation. However, we found that the kip operon encodes a functional oxoprolinase that facilitates detoxification of OP. Further, our data demonstrate that KipOTIA not only detoxifies OP, but also allows OP to be used as a nutrient source that supports the robust growth of C. difficile , thereby facilitating the conversion of a toxic byproduct of metabolism into an effective energy source.
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Wells KM, Ciftci Y, Peddinti BST, Ghiladi RA, Vediyappan G, Spontak RJ, Govind R. Preventing the spread of life-threatening gastrointestinal microbes on the surface of a continuously self-disinfecting block polymer. J Colloid Interface Sci 2023; 652:718-726. [PMID: 37611471 DOI: 10.1016/j.jcis.2023.08.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/03/2023] [Accepted: 08/12/2023] [Indexed: 08/25/2023]
Abstract
Highly persistent, drug-resistant and transmissible healthcare pathogens such as Clostridioides difficile (C. difficile) and Candida auris (C. auris) are responsible for causing antibiotic-associated fatal diarrhea and invasive candidiasis, respectively. In this study, we demonstrate that these potentially lethal gastrointestinal microbes can be rapidly inactivated on the solid surface of a self-disinfecting anionic block polymer that inherently generates a water surface layer that is highly acidic (pH < 1) upon hydration. Due to thermodynamic incompatibility between its chemical sequences, the polymer spontaneously self-organizes into a nanostructure that enables proton migration from the interior of a film to the surface via contiguous nanoscale hydrophilic channels, as discerned here by scanning electron and atomic force microscopies, as well as X-ray photoelectron spectroscopy. Here, we report that two strains of C. difficile in the vegetative state and two species of Candida, Candida albicans (C. albicans) and C. auris, are, in most cases, inactivated to the limit of minimum detection. Corresponding electron and optical microscopy images reveal that, upon exposure to the hydrated polymer, the outer microbial membranes display evidence of damage and intracellular material is expelled. Combined with our previous studies of rapid bacterial and viral inactivation, these antimicrobial results are highly encouraging and, if translatable to clinical conditions in the form of self-standing polymer films or coatings, are expected to benefit the welfare of patients in healthcare facilities by continuously preventing the spread of such potentially dangerous microbes.
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Affiliation(s)
- Kacie M Wells
- Fiber & Polymer Science Program, North Carolina State University, Raleigh, NC 27695, United States
| | - Yusuf Ciftci
- Division of Biology, Kansas State University, Manhattan, KS 66506, United States
| | - Bharadwaja S T Peddinti
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States
| | | | - Richard J Spontak
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States; Department of Materials Science & Engineering, North Carolina State University, Raleigh, NC 27695, United States.
| | - Revathi Govind
- Division of Biology, Kansas State University, Manhattan, KS 66506, United States.
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Dailey KM, Small JM, Pullan JE, Winfree S, Vance KE, Orr M, Mallik S, Bayles KW, Hollingsworth MA, Brooks AE. An intravenous pancreatic cancer therapeutic: Characterization of CRISPR/Cas9n-modified Clostridium novyi-Non Toxic. PLoS One 2023; 18:e0289183. [PMID: 37963142 PMCID: PMC10645340 DOI: 10.1371/journal.pone.0289183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/12/2023] [Indexed: 11/16/2023] Open
Abstract
Clostridium novyi has demonstrated selective efficacy against solid tumors largely due to the microenvironment contained within dense tumor cores. The core of a solid tumor is typically hypoxic, acidic, and necrotic-impeding the penetration of current therapeutics. C. novyi is attracted to the tumor microenvironment and once there, can both lyse and proliferate while simultaneously re-activating the suppressed immune system. C. novyi systemic toxicity is easily mitigated by knocking out the phage DNA plasmid encoded alpha toxin resulting in C. novyi-NT; but, after intravenous injection spores are quickly cleared by phagocytosis before accomplishing significant tumor localization. C. novyi-NT could be designed to accomplish intravenous delivery with the potential to target all solid tumors and their metastases in a single dose. This study characterizes CRISPR/Cas9 modified C. novyi-NT to insert the gene for RGD, a tumor targeting peptide, expressed within the promoter region of a spore coat protein. Expression of the RGD peptide on the outer spore coat of C. novyi-NT indicates an increased capacity for tumor localization of C. novyi upon intravenous introduction based on the natural binding of RGD with the αvβ3 integrin commonly overexpressed on the epithelial tissue surrounding a tumor, and lead to immune stimulation.
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Affiliation(s)
- Kaitlin M. Dailey
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, United States of America
- Cell and Molecular Biology Program, North Dakota State University, Fargo, ND, United States of America
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States of America
| | - James M. Small
- Department of Pathology and Microbiology, Rocky Vista University, Parker, CO, United States of America
| | - Jessica E. Pullan
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States of America
- Department of Physical Science, Southern Utah University, Cedar City, UT, United States of America
| | - Seth Winfree
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, United States of America
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Krysten E. Vance
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Megan Orr
- Department of Statistics, North Dakota State University, Fargo, ND, United States of America
- Center for Diagnostics and Therapeutic Strategies in Pancreatic Cancer Biostatistics Core Facility, North Dakota State University, Fargo, ND, United States of America
| | - Sanku Mallik
- Cell and Molecular Biology Program, North Dakota State University, Fargo, ND, United States of America
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Kenneth W. Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Michael A. Hollingsworth
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE, United States of America
| | - Amanda E. Brooks
- Cell and Molecular Biology Program, North Dakota State University, Fargo, ND, United States of America
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States of America
- Department of Research and Scholarly Activity, Rocky Vista University, Ivins, UT, United States of America
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Rizvi A, Vargas-Cuebas G, Edwards AN, DiCandia MA, Carter ZA, Lee CD, Monteiro MP, McBride SM. Glycine fermentation by C. difficile promotes virulence and spore formation, and is induced by host cathelicidin. Infect Immun 2023; 91:e0031923. [PMID: 37754683 PMCID: PMC10580938 DOI: 10.1128/iai.00319-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/28/2023] Open
Abstract
Clostridioides difficile is a leading cause of antibiotic-associated diarrheal disease. C. difficile colonization, growth, and toxin production in the intestine is strongly associated with its ability to use amino acids to generate energy, but little is known about the impact of specific amino acids on C. difficile pathogenesis. The amino acid glycine is enriched in the dysbiotic gut and is suspected to contribute to C. difficile infection. We hypothesized that the use of glycine as an energy source contributes to colonization of the intestine and pathogenesis of C. difficile. To test this hypothesis, we deleted the glycine reductase (GR) genes grdAB, rendering C. difficile unable to ferment glycine, and investigated the impact on growth and pathogenesis. Our data show that the grd pathway promotes growth, toxin production, and sporulation. Glycine fermentation also had a significant impact on toxin production and pathogenesis of C. difficile in the hamster model of disease. Furthermore, we determined that the grd locus is regulated by host cathelicidin (LL-37) and the cathelicidin-responsive regulator, ClnR, indicating that the host peptide signals to control glycine catabolism. The induction of glycine fermentation by LL-37 demonstrates a direct link between the host immune response and the bacterial reactions of toxin production and spore formation.
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Affiliation(s)
- Arshad Rizvi
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Germán Vargas-Cuebas
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Michael A. DiCandia
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Zavier A. Carter
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Cheyenne D. Lee
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Marcos P. Monteiro
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
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Baldassare MA, Bhattacharjee D, Coles JD, Nelson S, McCollum CA, Seekatz AM. Butyrate enhances Clostridioides difficile sporulation in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538596. [PMID: 37163089 PMCID: PMC10168334 DOI: 10.1101/2023.04.27.538596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Short chain fatty acids (SCFAs) are products of bacterial fermentation that help maintain important gut functions such as the intestinal barrier, signaling, and immune homeostasis. The main SCFAs acetate, propionate, and butyrate have demonstrated beneficial effects for the host, including importance in combatting infections caused by pathogens such as Clostridioides difficile . Despite the potential role of SCFAs in mitigating C. difficile infection, their direct effect on C. difficile remains unclear. Through a set of in vitro experiments, we investigated how SCFAs influence C. difficile growth, sporulation, and toxin production. Similar to previous studies, we observed that butyrate decreased growth of C. difficile strain 630 in a dose-dependent manner. The presence of butyrate also increased C. difficile sporulation, with minimal increases in toxin production. RNA-Seq analysis validated our experimental results, demonstrating increased expression of sporulation-related genes in conjunction with alternative metabolic and related C. difficile regulatory pathways, such as the carbon catabolite repressor, CcpA. Collectively, these data suggest that butyrate may signal alternative C. difficile metabolic pathways, thus modifying its growth and virulence to persist in the gut environment. IMPORTANCE Several studies suggest that butyrate may be important in alleviating gut infections, such as reducing inflammation caused by the healthcare-associated Clostridioides difficile . While studies in both animal models and human studies correlate high levels of butyrate with reduced C. difficile burden, the direct impact of butyrate on C. difficile remains unclear. Our study demonstrates that butyrate directly influences C. difficile by increasing its sporulation and modifying its metabolism, potentially using butyrate as a biomarker to shift survival strategies in a changing gut environment. These data point to additional therapeutic approaches to combat C. difficile in a butyrate-directed manner.
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DiCandia MA, Edwards AN, Lee CD, Monteiro MP, Cuebas GNV, Bagchi P, McBride SM. A Conserved Switch Controls Virulence, Sporulation, and Motility in C. difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534590. [PMID: 37034656 PMCID: PMC10081167 DOI: 10.1101/2023.03.28.534590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Spore formation is required for environmental survival and transmission of the human enteropathogenic Clostridioides difficile . In all bacterial spore formers, sporulation is regulated through activation of the master response regulator, Spo0A. However, the factors and mechanisms that directly regulate C. difficile Spo0A activity are not defined. In the well-studied Bacillus species, Spo0A is directly inactivated by Spo0E, a small phosphatase. To understand Spo0E function in C. difficile , we created a null mutation of the spo0E ortholog and assessed sporulation and physiology. The spo0E mutant produced significantly more spores, demonstrating Spo0E represses C. difficile sporulation. Unexpectedly, the spo0E mutant also exhibited increased motility and toxin production, and enhanced virulence in animal infections. We uncovered that Spo0E interacts with both Spo0A and the toxin and motility regulator, RstA. Direct interactions between Spo0A, Spo0E, and RstA constitute a previously unknown molecular switch that coordinates sporulation with motility and toxin production. Reinvestigation of Spo0E function in B. subtilis revealed that Spo0E induced motility, demonstrating Spo0E regulation of motility and sporulation among divergent species. Further, we found that Spo0E orthologs are widespread among prokaryotes, suggesting that Spo0E performs conserved regulatory functions in diverse bacteria.
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Wiese M, Schuren FHJ, Smits WK, Kuijper EJ, Ouwens A, Heerikhuisen M, Vigsnaes L, van den Broek TJ, de Boer P, Montijn RC, van der Vossen JMBM. 2'-Fucosyllactose inhibits proliferation of Clostridioides difficile ATCC 43599 in the CDi-screen, an in vitro model simulating Clostridioides difficile infection. Front Cell Infect Microbiol 2022; 12:991150. [PMID: 36389156 PMCID: PMC9650113 DOI: 10.3389/fcimb.2022.991150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/10/2022] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Clostridioides difficile is a Gram-positive anaerobic bacterium that can produce the toxins TcdA and/or TcdB and is considered an opportunistic pathogen. C. difficile is mainly transmitted as endospores, which germinate to produce the pathogenic vegetative cells under suitable conditions in the gut. To efficiently screen novel therapeutic- interventions against the proliferation of C. difficile within a complex microbial community, platforms are needed that facilitate parallel experimentation. In order to allow for screening of novel interventions a medium-to-high throughput in vitro system is desirable. To this end, we have developed the 96-well CDi-screen platform that employs an adapted simulated ileal effluent medium (CDi-SIEM) and allows for culturing of pathogenic C. difficile. METHODS C. difficile strain ATCC 43599 was inoculated in the form of vegetative cells and spores into the CDi-screen in the presence and absence of a cultured fecal microbiota and incubated for 48h. To demonstrate its utility, we investigated the effect of the human milk oligosaccharide 2'-Fucosyllactose (2'-FL) at 4 and 8 mg/mL on C. difficile outgrowth and toxin production in the CDi-screen. The test conditions were sampled after 24 and 48 hours. C. difficile -specific primers were used to monitor C. difficile growth via qPCR and barcoded 16S rRNA gene amplicon sequencing facilitated the in-depth analysis of gut microbial community dynamics. RESULTS C. difficile ATCC 43599 proliferated in CDi-SIEM, both when inoculated as spores and as vegetative cells. The strain reached cell numbers expressed as C. difficile genome equivalents of up to 10 8 cells per mL after 24h of incubation. 2'-FL significantly inhibited the outgrowth of the ATTC 43599 strain within a complex human gut microbial community in the CDi-screen. In addition, a dose-dependent modulation of the gut microbial community composition by 2'-FL supplementation was detected, with a significant increase in the relative abundance of the genus Blautia in the presence of 2'-FL. CONCLUSION The CDi-screen is suitable for studying C. difficile proliferation in a complex gut ecosystem and for screening for anti-pathogenic interventions that target C. difficile directly and/or indirectly through interactions with the gut microbiota. Different doses of compounds such as in this study the dose of the human milk oligosaccharide 2'-FL can be screened for efficacy in the inhibition of C. difficile proliferation.
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Affiliation(s)
- Maria Wiese
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, Netherlands
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Frank H. J. Schuren
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ed J. Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Anita Ouwens
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, Netherlands
| | - Margreet Heerikhuisen
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, Netherlands
| | - Louise Vigsnaes
- Glycom A/S—DSM Nutritional Products Ltd., Kogle Allé 4, Hørsholm, Denmark
- Department of Technology, Faculty of Health, University College Copenhagen, Copenhagen, Denmark
| | - Tim J. van den Broek
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, Netherlands
| | - Paulo de Boer
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, Netherlands
| | - Roy C. Montijn
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, Netherlands
| | - Jos M. B. M. van der Vossen
- Microbiology and Systems Biology, The Netherlands Organization for Applied Scientific Research (TNO), Leiden, Netherlands
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Calatayud M, Duysburgh C, Van den Abbeele P, Franckenstein D, Kuchina-Koch A, Marzorati M. Long-Term Lactulose Administration Improves Dysbiosis Induced by Antibiotic and C. difficile in the PathoGut TM SHIME Model. Antibiotics (Basel) 2022; 11:1464. [PMID: 36358119 PMCID: PMC9686563 DOI: 10.3390/antibiotics11111464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 09/28/2023] Open
Abstract
Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and an important nosocomial infection with different severity degrees. Disruption of the gut microbiota by broad-spectrum antibiotics creates a proper environment for C. difficile colonization, proliferation, and clinical disease onset. Restoration of the gut microbial ecosystem through prebiotic interventions can constitute an effective complementary treatment of CDI. Using an adapted simulator of the human gut microbial ecosystem, the PathoGutTM SHIME, the effect of different long-term and repeated dose lactulose treatments was tested on C. difficile germination and growth in antibiotic-induced dysbiotic gut microbiota environments. The results showed that lactulose reduced the growth of viable C. difficile cells following clindamycin treatment, shifted the antibiotic-induced dysbiotic microbial community, and stimulated the production of health-promoting metabolites (especially butyrate). Recovery of the gut microenvironment by long-term lactulose administration following CDI was also linked to lactate production, decrease in pH and modulation of bile salt metabolism. At a structural level, lactulose showed a significant bifidogenic potential and restored key commensal members of the gut ecosystem such as Lactobacillaceae, Veillonellaceae and Lachnospiraceae. These results support further human intervention studies aiming to validate the in vitro beneficial effects of lactulose on gut microbiome recovery during antibiotic exposure and CDI.
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Affiliation(s)
- Marta Calatayud
- ProDigest BV, Technologiepark 82, 9052 Ghent, Belgium
- Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | | | | | | | | | - Massimo Marzorati
- ProDigest BV, Technologiepark 82, 9052 Ghent, Belgium
- Center of Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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10
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Son YJ, Kim YR, Oh SH, Jung S, Ciufolini MA, Hwang HJ, Kwak JH, Pai H. Micrococcin P2 Targets Clostridioides difficile. JOURNAL OF NATURAL PRODUCTS 2022; 85:1928-1935. [PMID: 35816693 DOI: 10.1021/acs.jnatprod.2c00120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Clostridioides difficile infection is a global public health threat. Extensive in vitro assays using clinical isolates have identified micrococcin P2 (MP2, 1) as a particularly effective anti-C. difficile agent. MP2 possesses a mode of action that differs from other antibiotics and pharmacokinetic properties that render it especially promising. Its time-kill studies have been investigated using hypervirulent C. difficile ribotype 027. DSS (dextran sulfate sodium)-induced in vivo mouse studies with that strain indicate that 1 is better than vancomycin and fidaxomicin. Thus, micrococcin P2 is a valuable platform to be exploited for the development of new anti-C. difficile antibiotics.
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Affiliation(s)
- Young-Jin Son
- A&J Science Co., Ltd., 80 Chumbok Road, Dong Gu, Daegu, 41061, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, 1 Gwanak Road, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Young-Rok Kim
- School of Life Science, Handong Global University, 558 Handong Road, Heunghae-eup, Buk-gu, Pohang, 37554, Republic of Korea
| | - Sang-Hun Oh
- School of Life Science, Handong Global University, 558 Handong Road, Heunghae-eup, Buk-gu, Pohang, 37554, Republic of Korea
| | - Sungji Jung
- School of Life Science, Handong Global University, 558 Handong Road, Heunghae-eup, Buk-gu, Pohang, 37554, Republic of Korea
| | - Marco A Ciufolini
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6K 1Z1, Canada
| | - Hee-Jong Hwang
- A&J Science Co., Ltd., 80 Chumbok Road, Dong Gu, Daegu, 41061, Republic of Korea
| | - Jin-Hwan Kwak
- School of Life Science, Handong Global University, 558 Handong Road, Heunghae-eup, Buk-gu, Pohang, 37554, Republic of Korea
| | - Hyunjoo Pai
- Department of Internal Medicine, College of Medicine, Hanyang University, 222 Wangsimni Road, Seongdong-gu, Seoul, 04763, Republic of Korea
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11
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Pike CM, Tam J, Melnyk RA, Theriot CM. Tauroursodeoxycholic Acid Inhibits Clostridioides difficile Toxin-Induced Apoptosis. Infect Immun 2022; 90:e0015322. [PMID: 35862710 PMCID: PMC9387233 DOI: 10.1128/iai.00153-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/19/2022] [Indexed: 11/20/2022] Open
Abstract
C. difficile infection (CDI) is a highly inflammatory disease mediated by the production of two large toxins that weaken the intestinal epithelium and cause extensive colonic tissue damage. Antibiotic alternative therapies for CDI are urgently needed as current antibiotic regimens prolong the perturbation of the microbiota and lead to high disease recurrence rates. Inflammation is more closely correlated with CDI severity than bacterial burden, thus therapies that target the host response represent a promising yet unexplored strategy for treating CDI. Intestinal bile acids are key regulators of gut physiology that exert cytoprotective roles in cellular stress, inflammation, and barrier integrity, yet the dynamics between bile acids and host cellular processes during CDI have not been investigated. Here we show that several bile acids are protective against apoptosis caused by C. difficile toxins in Caco-2 cells and that protection is dependent on conjugation of bile acids. Out of 20 tested bile acids, taurine conjugated ursodeoxycholic acid (TUDCA) was the most potent inhibitor, yet unconjugated UDCA did not alter toxin-induced apoptosis. TUDCA treatment decreased expression of genes in lysosome associated and cytokine signaling pathways. TUDCA did not affect C. difficile growth or toxin activity in vitro whereas UDCA significantly reduced toxin activity in a Vero cell cytotoxicity assay and decreased tcdA gene expression. These results demonstrate that bile acid conjugation can have profound effects on C. difficile as well as the host and that conjugated and unconjugated bile acids may exert different therapeutic mechanisms against CDI.
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Affiliation(s)
- Colleen M. Pike
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - John Tam
- Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Roman A. Melnyk
- Molecular Medicine, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- SickKids Proteomics Analytics Robotics Chemical Biology Drug Discovery Facility, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Casey M. Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Response Regulator CD1688 Is a Negative Modulator of Sporulation in Clostridioides difficile. J Bacteriol 2022; 204:e0013022. [PMID: 35852332 PMCID: PMC9380558 DOI: 10.1128/jb.00130-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two-component signal transduction systems (TCSs), consisting of a sensor histidine kinase (HK) and a response regulator (RR), sense environmental stimuli and then modulate cellular responses, typically through changes in gene expression. Our previous work identified the DNA binding motif of CD1586, an RR implicated in Clostridioides difficile strain R20291 sporulation. To determine the role of this RR in the sporulation pathway in C. difficile, we generated a deletion strain of cd1688 in the historical 630 strain, the homolog of cd1586. The C. difficile Δcd1688 strain exhibited a hypersporulation phenotype, suggesting that CD1688 negatively regulates sporulation. Complementation of the C. difficile Δcd1688 strain restored sporulation. In contrast, a nonphosphorylatable copy of cd1688 did not restore sporulation to wild-type (WT) levels, indicating that CD1688 must be phosphorylated to properly modulate sporulation. Expression of the master regulator spo0A, the sporulation-specific sigma factors sigF, sigE, sigG, and sigK, and a signaling protein encoded by spoIIR was increased in the C. difficile Δcd1688 strain compared to WT. In line with the increased spoIIR expression, we detected an increase in mature SigE at an earlier time point, which arises from SpoIIR-mediated processing of pro-SigE. Taken together, our data suggest that CD1688 is a novel negative modulator of sporulation in C. difficile and contributes to mediating progression through the spore developmental pathway. These results add to our growing understanding of the complex regulatory events involved in C. difficile sporulation, insight that could be exploited for novel therapeutic development. IMPORTANCEClostridioides difficile causes severe gastrointestinal illness and is a leading cause of nosocomial infections in the United States. This pathogen produces metabolically dormant spores that are the major vehicle of transmission between hosts. The sporulation pathway involves an intricate regulatory network that controls a succession of morphological changes necessary to produce spores. The environmental signals inducing the sporulation pathway are not well understood in C. difficile. This work identified a response regulator, CD1688, that, when deleted, led to a hypersporulation phenotype, indicating that it typically acts to repress sporulation. Improving our understanding of the regulatory mechanisms modulating sporulation in C. difficile could provide novel strategies to eliminate or reduce spore production, thus decreasing transmission and disease relapse.
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13
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An engineered live biotherapeutic for the prevention of antibiotic-induced dysbiosis. Nat Biomed Eng 2022; 6:910-921. [PMID: 35411114 DOI: 10.1038/s41551-022-00871-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/18/2022] [Indexed: 02/08/2023]
Abstract
Antibiotic-induced alterations in the gut microbiota are implicated in many metabolic and inflammatory diseases, increase the risk of secondary infections and contribute to the emergence of antimicrobial resistance. Here we report the design and in vivo performance of an engineered strain of Lactococcus lactis that altruistically degrades the widely used broad-spectrum antibiotics β-lactams (which disrupt commensal bacteria in the gut) through the secretion and extracellular assembly of a heterodimeric β-lactamase. The engineered β-lactamase-expression system does not confer β-lactam resistance to the producer cell, and is encoded via a genetically unlinked two-gene biosynthesis strategy that is not susceptible to dissemination by horizontal gene transfer. In a mouse model of parenteral ampicillin treatment, oral supplementation with the engineered live biotherapeutic minimized gut dysbiosis without affecting the ampicillin concentration in serum, precluded the enrichment of antimicrobial resistance genes in the gut microbiome and prevented the loss of colonization resistance against Clostridioides difficile. Engineered live biotherapeutics that safely degrade antibiotics in the gut may represent a suitable strategy for the prevention of dysbiosis and its associated pathologies.
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14
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Huang J, Park GW, Jones RM, Fraser AM, Vinjé J, Jiang X. Efficacy of EPA-registered disinfectants against two human norovirus surrogates and Clostridioides difficile endospores. J Appl Microbiol 2022; 132:4289-4299. [PMID: 35279925 PMCID: PMC9119914 DOI: 10.1111/jam.15524] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 11/27/2022]
Abstract
AIMS To determine the efficacy of a panel of nine EPA-registered disinfectants against two human norovirus (HuNoV) surrogates (feline calicivirus [FCV] and Tulane virus [TuV]) and Clostridioides difficile endospores. METHODS AND RESULTS Nine EPA-registered products, five of which contained H2 O2 as active ingredient, were tested against infectious FCV, TuV and C. difficile endospores using two ASTM methods, a suspension and carrier test. Efficacy claims against FCV were confirmed for 8 of 9 products. The most efficacious product containing H2 O2 as ingredient achieved a >5.1 log reduction of FCV and >3.1 log reduction of TuV after 5 min, and >6.0 log reduction of C. difficile endospores after 10 min. Of the five products containing H2 O2 , no strong correlation (R2 = 0.25, p = 0.03) was observed between disinfection efficacy and H2 O2 concentration. Addition of 0.025% ferrous sulphate to 1% H2 O2 solution improved efficacy against FCV, TuV and C. difficile. CONCLUSION Disinfectants containing H2 O2 are the most efficacious disinfection products against FCV, TuV and C. difficile endospores. Product formulation, rather than the concentration of H2 O2 in a product, impacts the efficacy of a disinfection product. SIGNIFICANCE AND IMPACT OF STUDY H2 O2 -based disinfectants are efficacious against surrogate viruses for HuNoV and C. difficile endospores.
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Affiliation(s)
- Jinge Huang
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
| | - Geun Woo Park
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rachael M. Jones
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Angela M. Fraser
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Xiuping Jiang
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
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15
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Trzilova D, Warren MAH, Gadda NC, Williams CL, Tamayo R. Flagellum and toxin phase variation impacts intestinal colonization and disease development in a mouse model of Clostridioides difficile infection. Gut Microbes 2022; 14:2038854. [PMID: 35192433 PMCID: PMC8890394 DOI: 10.1080/19490976.2022.2038854] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Clostridioides difficile is a major nosocomial pathogen that can cause severe, toxin-mediated diarrhea and pseudomembranous colitis. Recent work has shown that C. difficile exhibits heterogeneity in swimming motility and toxin production in vitro through phase variation by site-specific DNA recombination. The recombinase RecV reversibly inverts the flagellar switch sequence upstream of the flgB operon, leading to the ON/OFF expression of flagellum and toxin genes. How this phenomenon impacts C. difficile virulence in vivo remains unknown. We identified mutations in the right inverted repeat that reduced or prevented flagellar switch inversion by RecV. We introduced these mutations into C. difficile R20291 to create strains with the flagellar switch "locked" in either the ON or OFF orientation. These mutants exhibited a loss of flagellum and toxin phase variation during growth in vitro, yielding precisely modified mutants suitable for assessing virulence in vivo. In a hamster model of acute C. difficile infection, the phase-locked ON mutant caused greater toxin accumulation than the phase-locked OFF mutant but did not differ significantly in the ability to cause acute disease symptoms. In contrast, in a mouse model, preventing flagellum and toxin phase variation affected the ability of C. difficile to colonize the intestinal tract and to elicit weight loss, which is attributable to differences in toxin production during infection. These results show that the ability of C. difficile to phase vary flagella and toxins influences colonization and disease development and suggest that the phenotypic variants generated by flagellar switch inversion have distinct capacities for causing disease.
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Affiliation(s)
- Dominika Trzilova
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Mercedes A. H. Warren
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Nicole C. Gadda
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Caitlin L. Williams
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,CONTACT Rita Tamayo 125 Mason Farm Rd, CB #7290, Chapel Hill, NC27599-7290
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16
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Real-time quantitative PCR method for detection and quantification of Clostridioides difficile cells and spores. METHODS IN MICROBIOLOGY 2022; 196:106458. [DOI: 10.1016/j.mimet.2022.106458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/31/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022]
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17
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Williamson CHD, Stone NE, Nunnally AE, Roe CC, Vazquez AJ, Lucero SA, Hornstra H, Wagner DM, Keim P, Rupnik M, Janezic S, Sahl JW. Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations. Microb Genom 2022; 8. [PMID: 35166655 PMCID: PMC8942030 DOI: 10.1099/mgen.0.000742] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is a pathogen often associated with hospital-acquired infection or antimicrobial-induced disease; however, increasing evidence indicates infections can result from community or environmental sources. Most genomic sequencing of C. difficile has focused on clinical strains, although evidence is growing that C. difficile spores are widespread in soil and water in the environment. In this study, we sequenced 38 genomes collected from soil and water isolates in Flagstaff (AZ, USA) and Slovenia in an effort targeted towards environmental surveillance of C. difficile. At the average nucleotide identity (ANI) level, the genomes were divergent to C. difficile at a threshold consistent with different species. A phylogenetic analysis of these divergent genomes together with Clostridioides genomes available in public repositories confirmed the presence of three previously described, cryptic Clostridioides species and added two additional clades. One of the cryptic species (C-III) was almost entirely composed of Arizona and Slovenia genomes, and contained distinct sub-groups from each region (evidenced by SNP and gene-content differences). A comparative genomics analysis identified multiple unique coding sequences per clade, which can serve as markers for subsequent environmental surveys of these cryptic species. Homologues to the C. difficile toxin genes, tcdA and tcdB, were found in cryptic species genomes, although they were not part of the typical pathogenicity locus observed in C. difficile, and in silico PCR suggested that some would not amplify with widely used PCR diagnostic tests. We also identified gene homologues in the binary toxin cluster, including some present on phage and, for what is believed to be the first time, on a plasmid. All isolates were obtained from environmental samples, so the function and disease potential of these toxin homologues is currently unknown. Enzymatic profiles of a subset of cryptic isolates (n=5) demonstrated differences, suggesting that these isolates contain substantial metabolic diversity. Antimicrobial resistance (AMR) was observed across a subset of isolates (n=4), suggesting that AMR mechanisms are intrinsic to the genus, perhaps originating from a shared environmental origin. This study greatly expands our understanding of the genomic diversity of Clostridioides. These results have implications for C. difficile One Health research, for more sensitive C. difficile diagnostics, as well as for understanding the evolutionary history of C. difficile and the development of pathogenesis.
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Affiliation(s)
| | - Nathan E Stone
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Amalee E Nunnally
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Chandler C Roe
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Adam J Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Samantha A Lucero
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Heidie Hornstra
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Prvomajska Ulica 1, 2000 Maribor, Slovenia
| | - Sandra Janezic
- Faculty of Medicine, University of Maribor, Taborska 8, 2000 Maribor, Slovenia
| | - Jason William Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
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18
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Islam MI, Seo H, Redwan A, Kim S, Lee S, Siddiquee M, Song HY. In Vitro and In Vivo Anti- Clostridioides difficile Effect of a Probiotic Bacillus amyloliquefaciens Strain. J Microbiol Biotechnol 2022; 32:46-55. [PMID: 34675143 PMCID: PMC9628829 DOI: 10.4014/jmb.2107.07057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022]
Abstract
Clostridioides difficile infection (CDI) is a significant cause of hospital-acquired and antibiotic-mediated intestinal diseases and is a growing global public health concern. Overuse of antibiotics and their effect on normal intestinal flora has increased the incidence and severity of infections. Thus, the development of new, effective, and safe treatment options is a high priority. Here, we report a new probiotic strain, Bacillus amyloliquefaciens (BA PMC-80), and its in vitro/in vivo anti-C. difficile effect as a prospective novel candidate for replacing conventional antibiotics. BA PMC-80 showed a significant anti-C. difficile effect in coculture assay, and its cell-free supernatant (CFS) also exhibited a considerable anti-C. difficile effect with an 89.06 μg/ml 50% minimal inhibitory concentration (MIC) in broth microdilution assay. The CFS was stable and equally functional under different pHs, heat, and proteinase treatments. It also exhibited a high sensitivity against current antibiotics and no toxicity in subchronic toxicity testing in hamsters. Finally, BA PMC-80 showed a moderate effect in a hamster CDI model with reduced infection severity and delayed death. However, further studies are required to optimize the treatment condition of the hamster CDI model for better efficacy and identify the antimicrobial compound produced by BA PMC-80.
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Affiliation(s)
- Md Imtiazul Islam
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Hoonhee Seo
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Asma Redwan
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea
| | - Sukyung Kim
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Saebim Lee
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Mashuk Siddiquee
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea
| | - Ho-Yeon Song
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea,Corresponding author Phone: +82-41-570-2412 Fax: +82-41-577-2415 E-mail:
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19
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Romo JA, Kumamoto CA. Characterization of the Effects of Candida Gastrointestinal Colonization on Clostridioides difficile Infection in a Murine Model. Methods Mol Biol 2022; 2542:271-285. [PMID: 36008672 DOI: 10.1007/978-1-0716-2549-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The role of fungal colonizers of the gastrointestinal tract during disease states is not well understood. Antibiotic treatment renders patients highly susceptible to infection by the bacterial pathogen C. difficile while also leading to blooms in fungal commensals, setting the stage for trans-kingdom interactions. Here, we describe a murine model of Candida gastrointestinal colonization coupled to a C. difficile infection (CDI) model, the measurement of CFU of both organisms, and collection of cecum and colon contents for the purpose of quantifying C. difficile toxin production. Additionally, we describe how to induce and purify C. difficile spores.
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Affiliation(s)
- Jesús A Romo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Carol A Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
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20
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Identification of ClpP Dual Isoform Disruption as an Anti-sporulation Strategy for Clostridioides difficile. J Bacteriol 2021; 204:e0041121. [PMID: 34807726 DOI: 10.1128/jb.00411-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gram-positive bacterium Clostridioides difficile is a primary cause of hospital-acquired diarrhea, threatening both immunocompromised and healthy individuals. An important aspect of defining mechanisms that drive C. difficile persistence and virulence relies on developing a more complete understanding of sporulation. C. difficile sporulation is the single determinant of transmission and complicates treatment and prevention due to the chemical and physical resilience of spores. By extension, the identification of druggable targets that significantly attenuate sporulation would have a significant impact on thwarting C. difficile infection. Using a new CRISPR-Cas9 nickase genome editing methodology, stop codons were inserted early in the coding sequence for clpP1 and clpP2 to generate C. difficile mutants that no longer produced the corresponding isoforms of caseinolytic protease P (ClpP). The data show that genetic ablation of ClpP isoforms leads to altered sporulation phenotypes with the clpP1/clpP2 double mutant exhibiting asporogenic behavior. A small screen of known ClpP inhibitors in a fluorescence-based biochemical assay identified bortezomib as an inhibitor of C. difficile ClpP that produces dose-dependent inhibition of purified ClpP. Incubation of C. difficile cultures in the presence of bortezomib reveals anti-sporulation effects approaching that observed in the clpP1/clpP2 double mutant. This work identifies ClpP as a key contributor to C. difficile sporulation and provides compelling support for the pursuit of small molecule ClpP inhibitors as C. difficile anti-sporulating agents. IMPORTANCE Due to diverse roles of ClpP and the reliance of pathogens upon this system for infection, it has emerged as a target for antimicrobial development. Biology regulated by ClpP is organism-dependent and has not been defined in C. difficile. This work identifies ClpP as a key contributor to C. difficile sporulation and provides compelling support for the pursuit of small molecule ClpP inhibitors as anti-sporulating agents. The identification of new approaches and/or drug targets that reduce C. difficile sporulation would be transformative and are expected to find high utility in prophylaxis, transmission attenuation, and relapse prevention. Discovery of the ClpP system as a major driver to sporulation also provides a new avenue of inquiry for advancing the understanding of sporulation.
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21
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Vigsnaes LK, Ghyselinck J, Van den Abbeele P, McConnell B, Moens F, Marzorati M, Bajic D. 2'FL and LNnT Exert Antipathogenic Effects against C. difficile ATCC 9689 In Vitro, Coinciding with Increased Levels of Bifidobacteriaceae and/or Secondary Bile Acids. Pathogens 2021; 10:927. [PMID: 34451391 PMCID: PMC8402123 DOI: 10.3390/pathogens10080927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile (formerly Clostridium difficile) infection (CDI) is one of the most common hospital-acquired infections, which is often triggered by a dysbiosed indigenous gut microbiota (e.g., upon antibiotic therapy). Symptoms can be as severe as life-threatening colitis. The current study assessed the antipathogenic potential of human milk oligosaccharides (HMOs), i.e., 2'-O-fucosyllactose (2'FL), lacto-N-neotetraose (LNnT), and a combination thereof (MIX), against C. difficile ATCC 9689 using in vitro gut models that allowed the evaluation of both direct and, upon microbiota modulation, indirect effects. During a first 48 h fecal batch study, dysbiosis and CDI were induced by dilution of the fecal inoculum. For each of the three donors tested, C. difficile levels strongly decreased (with >4 log CFU/mL) upon treatment with 2'FL, LNnT and MIX versus untreated blanks, coinciding with increased acetate/Bifidobacteriaceae levels. Interindividual differences among donors at an intermediate time point suggested that the antimicrobial effect was microbiota-mediated rather than being a direct effect of the HMOs. During a subsequent 11 week study with the PathogutTM model (specific application of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME®)), dysbiosis and CDI were induced by clindamycin (CLI) treatment. Vancomycin (VNC) treatment cured CDI, but the further dysbiosis of the indigenous microbiota likely contributed to CDI recurrence. Upon co-supplementation with VNC, both 2'FL and MIX boosted microbial activity (acetate and to lesser extent propionate/butyrate). Moreover, 2'FL avoided CDI recurrence, potentially because of increased secondary bile acid production. Overall, while not elucidating the exact antipathogenic mechanisms-of-action, the current study highlights the potential of HMOs to combat CDI recurrence, help the gut microbial community recover after antibiotic treatment, and hence counteract the adverse effects of antibiotic therapies.
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Affiliation(s)
- Louise Kristine Vigsnaes
- Glycom A/S—DSM Nutritional Products Ltd., Kogle Allé 4, DK-2970 Hørsholm, Denmark; (L.K.V.); (B.M.)
- Department of Technology, Faculty of Health, University College Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Pieter Van den Abbeele
- ProDigest, 9052 Ghent, Belgium; (J.G.); (F.M.); (M.M.)
- Cryptobiotix, 9052 Ghent, Belgium;
| | - Bruce McConnell
- Glycom A/S—DSM Nutritional Products Ltd., Kogle Allé 4, DK-2970 Hørsholm, Denmark; (L.K.V.); (B.M.)
| | | | - Massimo Marzorati
- ProDigest, 9052 Ghent, Belgium; (J.G.); (F.M.); (M.M.)
- Center of Microbial Ecology and Technology (CMET), Ghent University, 9000 Ghent, Belgium
| | - Danica Bajic
- Glycom A/S—DSM Nutritional Products Ltd., Kogle Allé 4, DK-2970 Hørsholm, Denmark; (L.K.V.); (B.M.)
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22
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Metabolic Labeling of Clostridioides difficile Proteins. Methods Mol Biol 2021. [PMID: 33950497 DOI: 10.1007/978-1-0716-1024-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The introduction of stable isotopes in vivo via metabolic labeling approaches (SILAC or 15N-labeling) allows, after combination of differentially treated labeled and unlabeled cells or protein extracts, for correction of protein quantification errors implemented during elaborated sample preparation workflows. The SILAC-based approach uses heavy arginine and lysine to incorporate the label into bacterial strains and cell lines, whereas 15N-metabolic labeling is achieved by cultivation in 15N-salt containing media. In case of Clostridioides difficile, the lack in arginine and lysine auxotrophy as well as the Stickland dominated metabolism makes metabolic labeling challenging. Here, a step-by-step guideline for the metabolic labeling of C. difficile is described, which combines cultivation in liquid 15N-substituted medium followed by cultivation steps on solid 15N-substituted medium. The described procedure results in a label incorporation rate higher than 97%. Cells prepared by the following method can be used as standard for relative quantification approaches of, e.g., the membrane or surface proteome of C. difficile.
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23
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Chen P, Zeng J, Liu Z, Thaker H, Wang S, Tian S, Zhang J, Tao L, Gutierrez CB, Xing L, Gerhard R, Huang L, Dong M, Jin R. Structural basis for CSPG4 as a receptor for TcdB and a therapeutic target in Clostridioides difficile infection. Nat Commun 2021; 12:3748. [PMID: 34145250 PMCID: PMC8213806 DOI: 10.1038/s41467-021-23878-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022] Open
Abstract
C. difficile is a major cause of antibiotic-associated gastrointestinal infections. Two C. difficile exotoxins (TcdA and TcdB) are major virulence factors associated with these infections, and chondroitin sulfate proteoglycan 4 (CSPG4) is a potential receptor for TcdB, but its pathophysiological relevance and the molecular details that govern recognition remain unknown. Here, we determine the cryo-EM structure of a TcdB–CSPG4 complex, revealing a unique binding site spatially composed of multiple discontinuous regions across TcdB. Mutations that selectively disrupt CSPG4 binding reduce TcdB toxicity in mice, while CSPG4-knockout mice show reduced damage to colonic tissues during C. difficile infections. We further show that bezlotoxumab, the only FDA approved anti-TcdB antibody, blocks CSPG4 binding via an allosteric mechanism, but it displays low neutralizing potency on many TcdB variants from epidemic hypervirulent strains due to sequence variations in its epitopes. In contrast, a CSPG4-mimicking decoy neutralizes major TcdB variants, suggesting a strategy to develop broad-spectrum therapeutics against TcdB. Chondroitin sulfate proteoglycan 4 (CSPG4) is a potential receptor for C. difficile toxin B (TcdB) during C. difficile infections (CDIs). Here, the cryo-EM structure of a TcdB–CSPG4 complex and CDI mouse models offer insights into CSPG4 role in CDIs and suggest a therapeutic strategy targeting TcdB.
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Affiliation(s)
- Peng Chen
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Ji Zeng
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Zheng Liu
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Hatim Thaker
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Siyu Wang
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA.,Department of Gastrointestinal, Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Songhai Tian
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Jie Zhang
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Liang Tao
- Center for Infectious Disease Research, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Craig B Gutierrez
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Li Xing
- UC Irvine Materials Research Institute (IMRI), University of California, Irvine, CA, USA
| | - Ralf Gerhard
- Institute of Toxicology, Hannover Medical School, Hannover, Germany
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Microbiology, Harvard Medical School, Boston, MA, USA. .,Department of Surgery, Harvard Medical School, Boston, MA, USA.
| | - Rongsheng Jin
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA.
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24
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Martins D, DiCandia MA, Mendes AL, Wetzel D, McBride SM, Henriques AO, Serrano M. CD25890, a conserved protein that modulates sporulation initiation in Clostridioides difficile. Sci Rep 2021; 11:7887. [PMID: 33846410 PMCID: PMC8041843 DOI: 10.1038/s41598-021-86878-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/17/2021] [Indexed: 12/16/2022] Open
Abstract
Bacteria that reside in the gastrointestinal tract of healthy humans are essential for our health, sustenance and well-being. About 50-60% of those bacteria have the ability to produce resilient spores that are important for the life cycle in the gut and for host-to-host transmission. A genomic signature for sporulation in the human intestine was recently described, which spans both commensals and pathogens such as Clostridioides difficile and contains several genes of unknown function. We report on the characterization of a signature gene, CD25890, which, as we show is involved in the control of sporulation initiation in C. difficile under certain nutritional conditions. Spo0A is the main regulatory protein controlling entry into sporulation and we show that an in-frame deletion of CD25890 results in increased expression of spo0A per cell and increased sporulation. The effect of CD25890 on spo0A is likely indirect and mediated through repression of the sinRR´ operon. Deletion of the CD25890 gene, however, does not alter the expression of the genes coding for the cytotoxins or the genes involved in biofilm formation. Our results suggest that CD25890 acts to modulate sporulation in response to the nutrients present in the environment.
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Affiliation(s)
- Diogo Martins
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal
| | - Michael A DiCandia
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Aristides L Mendes
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal
| | - Daniela Wetzel
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Adriano O Henriques
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal
| | - Mónica Serrano
- Instituto de Tecnologia Química E Biológica António Xavier, Avenida da República, 2780-157, Oeiras, Portugal.
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25
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Dailey KM, Jacobson RI, Johnson PR, Woolery TJ, Kim J, Jansen RJ, Mallik S, Brooks AE. Methods and Techniques to Facilitate the Development of Clostridium novyi NT as an Effective, Therapeutic Oncolytic Bacteria. Front Microbiol 2021; 12:624618. [PMID: 33854487 PMCID: PMC8039391 DOI: 10.3389/fmicb.2021.624618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/28/2021] [Indexed: 12/17/2022] Open
Abstract
The tumor microenvironment is characterized by anomalous vascularization, hypoxia, and acidity at the core of solid tumors that culminates in concentrated necrosis and immune system dysregulation among other effects. While this environment presents several challenges for the development of oncotherapeutics that deliver their activity via the enhanced permeability and retention (EPR) effect of the leaky blood vessels around a tumor, oncolytic bacteria, or a class of bacteria with a noted capacity to lyse solid tumors, are attracted to the very environment found at the center of solid tumors that confounds other therapeutics. It is this capacity that allows for a potent, active penetration from the tumor margins into the core, and subsequent colonization to facilitate lysis and immune reactivation. Clostridium novyi in particular has recently shown great promise in preclinical and clinical trials when administered directly to the tumor. These studies indicate that C. novyi is uniquely poised to effectively accomplish the long sought after "holy grail" of oncotherapeutics: selective tumor localization via intravenous delivery. This study reports the development of efficient methods that facilitate experimental work and therapeutic translation of C. novyi including the ability to work with this obligate micro-anaerobe on the benchtop. Additionally, this study seeks to utilize this newfound experimental flexibility to address several gaps in the current knowledge regarding the efficacy of CRIPSR/Cas9-mediated gene insertion in this species to further develop this oncolytic bacteria and the genetic customization of bacteria in general.
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Affiliation(s)
- Kaitlin M Dailey
- Cell and Molecular Biology Program, North Dakota State University, Fargo, ND, United States.,Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States
| | - Reed I Jacobson
- Department of Biological Sciences, North Dakota State University, Fargo, ND, United States
| | - Paige R Johnson
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States
| | - Taylor J Woolery
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States
| | - Jiha Kim
- Department of Biological Sciences, North Dakota State University, Fargo, ND, United States
| | - Rick J Jansen
- Department of Public Health, North Dakota State University, Fargo, ND, United States.,Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, United States
| | - Sanku Mallik
- Cell and Molecular Biology Program, North Dakota State University, Fargo, ND, United States.,Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States
| | - Amanda E Brooks
- Cell and Molecular Biology Program, North Dakota State University, Fargo, ND, United States.,Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States.,Office of Research and Scholarly Activity, Rocky Vista University, Ivins, UT, United States
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26
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Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota. Nat Commun 2021; 12:462. [PMID: 33469019 PMCID: PMC7815924 DOI: 10.1038/s41467-020-20746-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 12/17/2020] [Indexed: 01/04/2023] Open
Abstract
Clostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile. Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile. We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation. The effects of antibiotics on the gut microbiota can lead to enhanced colonization of Clostridioides difficile (C. difficile) and toxin-mediated pathogenesis. Here, using defined toxin-mutant strains and a murine model, the authors provide insights into how toxin-induced inflammation alters C. difficile metabolism, host tissue gene expression and gut microbiota, together influencing a beneficial niche for infection.
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27
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Faecal microbiota transplantation for Clostridioides difficile: mechanisms and pharmacology. Nat Rev Gastroenterol Hepatol 2021; 18:67-80. [PMID: 32843743 DOI: 10.1038/s41575-020-0350-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
Faecal microbiota transplantation (FMT) has emerged as a remarkably successful treatment for recurrent Clostridioides difficile infection that cannot be cured with antibiotics alone. Understanding the complex biology and pathogenesis of C. difficile infection, which we discuss in this Perspective, is essential for understanding the potential mechanisms by which FMT cures this disease. Although FMT has already entered clinical practice, different microbiota-based products are currently in clinical trials and are vying for regulatory approval. However, all these therapeutics belong to an entirely new class of agents that require the development of a new branch of pharmacology. Characterization of microbiota therapeutics uses novel and rapidly evolving technologies and requires incorporation of microbial ecology concepts. Here, we consider FMT within a pharmacological framework, including its essential elements: formulation, pharmacokinetics and pharmacodynamics. From this viewpoint, multiple gaps in knowledge become apparent, identifying areas that require systematic research. This knowledge is needed to help clinical providers use microbiota therapeutics appropriately and to facilitate development of next-generation microbiota products with improved safety and efficacy. The discussion here is limited to FMT as a representative of microbiota therapeutics and recurrent C. difficile as the indication; however, consideration of the intrinsic basic principles is relevant to this entire class of microbiota-based therapeutics.
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28
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Combined and Distinct Roles of Agr Proteins in Clostridioides difficile 630 Sporulation, Motility, and Toxin Production. mBio 2020; 11:mBio.03190-20. [PMID: 33443122 PMCID: PMC8534292 DOI: 10.1128/mbio.03190-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Clostridioides difficile accessory gene regulator 1 (agr1) locus consists of two genes, agrB1 and agrD1, that presumably constitute an autoinducing peptide (AIP) system. Typically, AIP systems function through the AgrB-mediated processing of AgrD to generate a processed form of the AIP that provides a concentration-dependent extracellular signal. Here, we show that the C. difficile 630 Agr1 system has multiple functions, not all of which depend on AgrB1. CRISPR-Cas9n deletion of agrB1, agrD1, or the entire locus resulted in changes in transcription of sporulation-related factors and an overall loss in spore formation. Sporulation was recovered in the mutants by providing supernatant from stationary-phase cultures of the parental strain. In contrast, C. difficile motility was reduced only when both AgrB1 and AgrD1 were disrupted. Finally, in the absence of AgrB1, the AgrD1 peptide accumulated within the cytoplasm and this correlated with increased expression of tcdR (15-fold), as well as tcdA (20-fold) and tcdB (5-fold), which encode the two major C. difficile toxins. The combined deletion of agrB1/agrD1 or deletion of only agrD1 did not significantly alter expression of tcdR or tcdB but did show a minor effect on tcdA expression. Overall, these data indicate that the Agr1-based system in C. difficile 630 carries out multiple functions, some of which are associated with prototypical AIP signaling and others of which involve previously undescribed mechanisms of action.IMPORTANCE C. difficile is a spore-forming, toxigenic, anaerobic bacterium that causes severe gastrointestinal illness. Understanding the ways in which C. difficile senses growth conditions to regulate toxin expression and sporulation is essential to advancing our understanding of this pathogen. The Agr1 system in C. difficile has been thought to function by generating an extracellular autoinducing peptide that accumulates and exogenously activates two-component signaling. The absence of the peptide or protease should, in theory, result in similar phenotypes. However, in contrast to longstanding assumptions about Agr, we found that mutants of individual agr1 genes exhibit distinct phenotypes in C. difficile These findings suggest that the Agr1 system may have other regulatory mechanisms independent of the typical Agr quorum sensing system. These data not only challenge models for Agr's mechanism of action in C. difficile but also may expand our conceptions of how this system works in other Gram-positive pathogens.
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29
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Naclerio GA, Abutaleb NS, Li D, Seleem MN, Sintim HO. Ultrapotent Inhibitor of Clostridioides difficile Growth, Which Suppresses Recurrence In Vivo. J Med Chem 2020; 63:11934-11944. [PMID: 32960605 DOI: 10.1021/acs.jmedchem.0c01198] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clostridioides difficile is the leading cause of healthcare-associated infection in the U.S. and considered an urgent threat by the Centers for Disease Control and Prevention (CDC). Only two antibiotics, vancomycin and fidaxomicin, are FDA-approved for the treatment of C. difficile infection (CDI), but these therapies still suffer from high treatment failure and recurrence. Therefore, new chemical entities to treat CDI are needed. Trifluoromethylthio-containing N-(1,3,4-oxadiazol-2-yl)benzamides displayed very potent activities [sub-μg/mL minimum inhibitory concentration (MIC) values] against Gram-positive bacteria. Here, we report remarkable antibacterial activity enhancement via halogen substitutions, which afforded new anti-C. difficile agents with ultrapotent activities [MICs as low as 0.003 μg/mL (0.007 μM)] that surpassed the activity of vancomycin against C. difficile clinical isolates. The most promising compound in the series, HSGN-218, is nontoxic to mammalian colon cells and is gut-restrictive. In addition, HSGN-218 protected mice from CDI recurrence. Not only does this work provide a potential clinical lead for the development of C. difficile therapeutics but also highlights dramatic drug potency enhancement via halogen substitution.
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Affiliation(s)
- George A Naclerio
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
| | - Nader S Abutaleb
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, United States
| | - Daoyi Li
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, United States
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, Indiana 47907, United States.,Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24060, United States.,Purdue Institute of Inflammation, Immunology, and Infectious Disease, West Lafayette, Indiana 47907, United States
| | - Herman O Sintim
- Chemistry Department, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States.,Purdue Institute of Inflammation, Immunology, and Infectious Disease, West Lafayette, Indiana 47907, United States
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30
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Nasal Immunization with the C-Terminal Domain of Bcla3 Induced Specific IgG Production and Attenuated Disease Symptoms in Mice Infected with Clostridioides difficile Spores. Int J Mol Sci 2020; 21:ijms21186696. [PMID: 32933117 PMCID: PMC7555657 DOI: 10.3390/ijms21186696] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile is a Gram-positive, spore-forming bacterium that causes a severe intestinal infection. Spores of this pathogen enter in the human body through the oral route, interact with intestinal epithelial cells and persist in the gut. Once germinated, the vegetative cells colonize the intestine and produce toxins that enhance an immune response that perpetuate the disease. Therefore, spores are major players of the infection and ideal targets for new therapies. In this context, spore surface proteins of C. difficile, are potential antigens for the development of vaccines targeting C. difficile spores. Here, we report that the C-terminal domain of the spore surface protein BclA3, BclA3CTD, was identified as an antigenic epitope, over-produced in Escherichia coli and tested as an immunogen in mice. To increase antigen stability and efficiency, BclA3CTD was also exposed on the surface of B. subtilis spores, a mucosal vaccine delivery system. In the experimental conditions used in this study, free BclA3CTD induced antibody production in mice and attenuated some C. difficile infection symptoms after a challenge with the pathogen, while the spore-displayed antigen resulted less effective. Although dose regimen and immunization routes need to be optimized, our results suggest BclA3CTD as a potentially effective antigen to develop a new vaccination strategy targeting C. difficile spores.
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31
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Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackermann Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, Church GM, Brown ED, Jaakkola TS, Barzilay R, Collins JJ. A Deep Learning Approach to Antibiotic Discovery. Cell 2020; 180:688-702.e13. [PMID: 32084340 DOI: 10.1016/j.cell.2020.01.021] [Citation(s) in RCA: 692] [Impact Index Per Article: 173.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 02/06/2023]
Abstract
Due to the rapid emergence of antibiotic-resistant bacteria, there is a growing need to discover new antibiotics. To address this challenge, we trained a deep neural network capable of predicting molecules with antibacterial activity. We performed predictions on multiple chemical libraries and discovered a molecule from the Drug Repurposing Hub-halicin-that is structurally divergent from conventional antibiotics and displays bactericidal activity against a wide phylogenetic spectrum of pathogens including Mycobacterium tuberculosis and carbapenem-resistant Enterobacteriaceae. Halicin also effectively treated Clostridioides difficile and pan-resistant Acinetobacter baumannii infections in murine models. Additionally, from a discrete set of 23 empirically tested predictions from >107 million molecules curated from the ZINC15 database, our model identified eight antibacterial compounds that are structurally distant from known antibiotics. This work highlights the utility of deep learning approaches to expand our antibiotic arsenal through the discovery of structurally distinct antibacterial molecules.
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Affiliation(s)
- Jonathan M Stokes
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin Yang
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kyle Swanson
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wengong Jin
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andres Cubillos-Ruiz
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Nina M Donghia
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Craig R MacNair
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Shawn French
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Lindsey A Carfrae
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Zohar Bloom-Ackermann
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Victoria M Tran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anush Chiappino-Pepe
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ahmed H Badran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ian W Andrews
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Emma J Chory
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Tommi S Jaakkola
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Regina Barzilay
- Machine Learning for Pharmaceutical Discovery and Synthesis Consortium, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - James J Collins
- Department of Biological Engineering, Synthetic Biology Center, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Abdul Latif Jameel Clinic for Machine Learning in Health, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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32
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Trzilova D, Anjuwon-Foster BR, Torres Rivera D, Tamayo R. Rho factor mediates flagellum and toxin phase variation and impacts virulence in Clostridioides difficile. PLoS Pathog 2020; 16:e1008708. [PMID: 32785266 PMCID: PMC7446863 DOI: 10.1371/journal.ppat.1008708] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/24/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
The intestinal pathogen Clostridioides difficile exhibits heterogeneity in motility and toxin production. This phenotypic heterogeneity is achieved through phase variation by site-specific recombination via the DNA recombinase RecV, which reversibly inverts the “flagellar switch” upstream of the flgB operon. A recV mutation prevents flagellar switch inversion and results in phenotypically locked strains. The orientation of the flagellar switch influences expression of the flgB operon post-transcription initiation, but the specific molecular mechanism is unknown. Here, we report the isolation and characterization of spontaneous suppressor mutants in the non-motile, non-toxigenic recV flg OFF background that regained motility and toxin production. The restored phenotypes corresponded with increased expression of flagellum and toxin genes. The motile suppressor mutants contained single-nucleotide polymorphisms (SNPs) in rho, which encodes the bacterial transcription terminator Rho factor. Analyses using transcriptional reporters indicate that Rho contributes to heterogeneity in flagellar gene expression by preferentially terminating transcription of flg OFF mRNA within the 5’ leader sequence. Additionally, Rho is important for initial colonization of the intestine in a mouse model of infection, which may in part be due to the sporulation and growth defects observed in the rho mutants. Together these data implicate Rho factor as a regulator of gene expression affecting phase variation of important virulence factors of C. difficile. Phenotypic heterogeneity maintained by phase variation allows bacterial subpopulations to overcome potentially detrimental stresses in the environment, contributing to bacterial survival. Phase variation of flagella and toxins in C. difficile suggests that maintaining heterogeneity of their production may be important for survival and virulence. In this study, we identified Rho as a trans-acting factor that mediates the differential gene expression that imparts heterogeneity in flagellum and toxin production. These results reveal a new role for Rho-mediated transcription termination in regulation of gene expression.
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Affiliation(s)
- Dominika Trzilova
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Brandon R. Anjuwon-Foster
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Dariana Torres Rivera
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Convenient Protocol for Production and Purification of Clostridioides difficile Spores for Germination Studies. STAR Protoc 2020; 1:100071. [PMID: 33111107 PMCID: PMC7580112 DOI: 10.1016/j.xpro.2020.100071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Clostridioides difficile, an obligate anaerobic bacterium, causes infections leading to prolonged diarrhea. The bacterium produces dormant spores that can withstand an aerobic environment, resulting in easy environmental transfer. Here, we present a convenient sporulation and purification protocol that can be practiced in any lab setting using a portable anaerobic glove bag. This protocol also optimizes existing cell growth methods and presents a detailed trouble shooting guide. This protocol is a modification of those previously reported by Edwards and McBride (2016) and Shen et al. (2016).
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Abutaleb NS, Seleem MN. Auranofin, at clinically achievable dose, protects mice and prevents recurrence from Clostridioides difficile infection. Sci Rep 2020; 10:7701. [PMID: 32382070 PMCID: PMC7206065 DOI: 10.1038/s41598-020-64882-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022] Open
Abstract
Clostridioides difficile is the leading cause of nosocomial infections and a worldwide urgent public health threat. Without doubt, there is an urgent need for new effective anticlostridial agents due to the increasing incidence and severity of C. difficile infection (CDI). The aim of the present study is to investigate the in vivo efficacy of auranofin (rheumatoid arthritis FDA-approved drug) in a CDI mouse model and establish an adequate dosage for treatment. The effects of increased C. difficile inoculum, and pre-exposure to simulated gastric intestinal fluid (SGF) and simulated intestinal fluid (SIF), on the antibacterial activity of auranofin were investigated. Auranofin's in vitro antibacterial activity was stable in the presence of high bacterial inoculum size compared to vancomycin and fidaxomicin. Moreover, it maintained its anti-C. difficile activity after being exposed to SGF and SIF. Upon testing in a CDI mouse model, auranofin at low clinically achievable doses (0.125 mg/kg and 0.25 mg/kg) significantly protected mice against CDI with 100% and 80% survival, respectively. Most importantly, auranofin (0.125 mg/kg and 0.25 mg/kg) significantly prevented CDI recurrence when compared with vancomycin. Collectively, these results indicate that auranofin could potentially provide an effective, safe and quick supplement to the current approaches for treating CDI.
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Affiliation(s)
- Nader S Abutaleb
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, 47907, USA
| | - Mohamed N Seleem
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, 47907, USA.
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, West Lafayette, IN, 47907, USA.
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Selle K, Fletcher JR, Tuson H, Schmitt DS, McMillan L, Vridhambal GS, Rivera AJ, Montgomery SA, Fortier LC, Barrangou R, Theriot CM, Ousterout DG. In Vivo Targeting of Clostridioides difficile Using Phage-Delivered CRISPR-Cas3 Antimicrobials. mBio 2020; 11:e00019-20. [PMID: 32156803 PMCID: PMC7064742 DOI: 10.1128/mbio.00019-20] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/23/2020] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile is an important nosocomial pathogen that causes approximately 500,000 cases of C. difficile infection (CDI) and 29,000 deaths annually in the United States. Antibiotic use is a major risk factor for CDI because broad-spectrum antimicrobials disrupt the indigenous gut microbiota, decreasing colonization resistance against C. difficile Vancomycin is the standard of care for the treatment of CDI, likely contributing to the high recurrence rates due to the continued disruption of the gut microbiota. Thus, there is an urgent need for the development of novel therapeutics that can prevent and treat CDI and precisely target the pathogen without disrupting the gut microbiota. Here, we show that the endogenous type I-B CRISPR-Cas system in C. difficile can be repurposed as an antimicrobial agent by the expression of a self-targeting CRISPR that redirects endogenous CRISPR-Cas3 activity against the bacterial chromosome. We demonstrate that a recombinant bacteriophage expressing bacterial genome-targeting CRISPR RNAs is significantly more effective than its wild-type parent bacteriophage at killing C. difficile both in vitro and in a mouse model of CDI. We also report that conversion of the phage from temperate to obligately lytic is feasible and contributes to the therapeutic suitability of intrinsic C. difficile phages, despite the specific challenges encountered in the disease phenotypes of phage-treated animals. Our findings suggest that phage-delivered programmable CRISPR therapeutics have the potential to leverage the specificity and apparent safety of phage therapies and improve their potency and reliability for eradicating specific bacterial species within complex communities, offering a novel mechanism to treat pathogenic and/or multidrug-resistant organisms.IMPORTANCEClostridioides difficile is a bacterial pathogen responsible for significant morbidity and mortality across the globe. Current therapies based on broad-spectrum antibiotics have some clinical success, but approximately 30% of patients have relapses, presumably due to the continued perturbation to the gut microbiota. Here, we show that phages can be engineered with type I CRISPR-Cas systems and modified to reduce lysogeny and to enable the specific and efficient targeting and killing of C. difficilein vitro and in vivo. Additional genetic engineering to disrupt phage modulation of toxin expression by lysogeny or other mechanisms would be required to advance a CRISPR-enhanced phage antimicrobial for C. difficile toward clinical application. These findings provide evidence into how phage can be combined with CRISPR-based targeting to develop novel therapies and modulate microbiomes associated with health and disease.
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Affiliation(s)
- Kurt Selle
- Locus Biosciences, Inc., Morrisville, North Carolina, USA
| | - Joshua R Fletcher
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Hannah Tuson
- Locus Biosciences, Inc., Morrisville, North Carolina, USA
| | | | - Lana McMillan
- Locus Biosciences, Inc., Morrisville, North Carolina, USA
| | | | - Alissa J Rivera
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Stephanie A Montgomery
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Rodolphe Barrangou
- Locus Biosciences, Inc., Morrisville, North Carolina, USA
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Casey M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Induction of a Specific Humoral Immune Response by Nasal Delivery of Bcla2 ctd of Clostridioides difficile. Int J Mol Sci 2020; 21:ijms21041277. [PMID: 32074955 PMCID: PMC7072882 DOI: 10.3390/ijms21041277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/21/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile, formerly known as Clostridium difficile, is a spore-forming bacterium considered as the most common cause of nosocomial infections in developed countries. The spore of C. difficile is involved in the transmission of the pathogen and in its first interaction with the host; therefore, a therapeutic approach able to control C. difficile spores would improve the clearance of the infection. The C-terminal (CTD) end of BclA2, a spore surface protein of C. difficile responsible of the interaction with the host intestinal cells, was selected as a putative mucosal antigen. The BclA2 fragment, BclA2CTD, was purified and used to nasally immunize mice both as a free protein and after adsorption to the spore of Bacillus subtilis, a well-established mucosal delivery vehicle. While the adsorption to spores increased the in vitro stability of BclA2CTD, in vivo both free and spore-adsorbed BclA2CTD were able to induce a similar, specific humoral immune response in a murine model. Although in the experimental conditions utilized the immune response was not protective, the induction of specific IgG indicates that free or spore-bound BclA2CTD could act as a putative mucosal antigen targeting C. difficile spores.
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The Impact of pH on Clostridioides difficile Sporulation and Physiology. Appl Environ Microbiol 2020; 86:AEM.02706-19. [PMID: 31811041 DOI: 10.1128/aem.02706-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is a pathogenic bacterium that infects the human colon to cause diarrheal disease. Growth of the bacterium is known to be dependent on certain bile acids, oxygen levels, and nutrient availability in the intestine, but how the environmental pH can influence C. difficile is mostly unknown. Previous studies indicated that C. difficile modulates the intestinal pH, and prospective cohort studies have found a strong association between a more alkaline fecal pH and C. difficile infection. Based on these data, we hypothesized that C. difficile physiology can be affected by various pH conditions. In this study, we investigated the impact of a range of pH conditions on C. difficile to assess potential effects on growth, sporulation, motility, and toxin production in the strains 630Δerm and R20291. We observed pH-dependent differences in sporulation rate, spore morphology, and viability. Sporulation frequency was lowest under acidic conditions, and differences in cell morphology were apparent at low pH. In alkaline environments, C. difficile sporulation was greater for strain 630Δerm, whereas R20291 produced relatively high levels of spores in a broad range of pH conditions. Rapid changes in pH during exponential growth impacted sporulation similarly among the strains. Furthermore, we observed an increase in C. difficile motility with increases in pH, and strain-dependent differences in toxin production under acidic conditions. The data demonstrate that pH is an important parameter that affects C. difficile physiology and may reveal relevant insights into the growth and dissemination of this pathogen.IMPORTANCE Clostridioides difficile is an anaerobic bacterium that causes gastrointestinal disease. C. difficile forms dormant spores which can survive harsh environmental conditions, allowing their spread to new hosts. In this study, we determine how intestinally relevant pH conditions impact C. difficile physiology in the two divergent strains, 630Δerm and R20291. Our data demonstrate that low pH conditions reduce C. difficile growth, sporulation, and motility. However, toxin production and spore morphology were differentially impacted in the two strains at low pH. In addition, we observed that alkaline environments reduce C. difficile growth, but increase cell motility. When pH was adjusted rapidly during growth, we observed similar impacts on both strains. This study provides new insights into the phenotypic diversity of C. difficile grown under diverse pH conditions present in the intestinal tract, and demonstrates similarities and differences in the pH responses of different C. difficile isolates.
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Muñoz M, Restrepo-Montoya D, Kumar N, Iraola G, Herrera G, Ríos-Chaparro DI, Díaz-Arévalo D, Patarroyo MA, Lawley TD, Ramírez JD. Comparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum. Virulence 2019; 10:657-676. [PMID: 31304854 PMCID: PMC6629180 DOI: 10.1080/21505594.2019.1637699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/23/2019] [Accepted: 06/25/2019] [Indexed: 01/23/2023] Open
Abstract
Some well-known Clostridiales species such as Clostridium difficile and C. perfringens are agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as Clostridium tertium and C. paraputrificum. Three fecal isolates were identified as Clostridium tertium (Gcol.A2 and Gcol.A43) and C. paraputrificum (Gcol.A11) during public health screening for C. difficile infections in Colombia. C. paraputrificum genomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the C. tertium genomes than in the C. paraputrificum genomes. C. difficile tcdA and tcdB toxins encoding homologous sequences and other potential virulence factors were also identified. EndoA interferase, a toxic component of the type II toxin-antitoxin system, was found among the C. tertium genomes. toxA was the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the C. tertium genomes compared with the C. paraputrificum genomes (33.3 and 28.4 on average, respectively). This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in C. paraputrificum), with proteins involved in sporulation processes more highly represented in C. tertium. These finding suggest the need to advance in the study of those species with potential importance at public health level.
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Affiliation(s)
- Marina Muñoz
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Posgrado Interfacultades, Doctorado en Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel Restrepo-Montoya
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, USA
| | - Nitin Kumar
- Host–Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, Montevideo, Uruguay
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile
| | - Giovanny Herrera
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Dora I. Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Diana Díaz-Arévalo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Faculty of Animal Sciences, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
| | - Manuel A. Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Trevor D. Lawley
- Host–Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas – UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
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Phase variation of a signal transduction system controls Clostridioides difficile colony morphology, motility, and virulence. PLoS Biol 2019; 17:e3000379. [PMID: 31658249 PMCID: PMC6837544 DOI: 10.1371/journal.pbio.3000379] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 11/07/2019] [Accepted: 10/15/2019] [Indexed: 12/20/2022] Open
Abstract
Recent work has revealed that Clostridioides difficile, a major cause of nosocomial diarrheal disease, exhibits phenotypic heterogeneity within a clonal population as a result of phase variation. Many C. difficile strains representing multiple ribotypes develop two colony morphotypes, termed rough and smooth, but the biological implications of this phenomenon have not been explored. Here, we examine the molecular basis and physiological relevance of the distinct colony morphotypes produced by this bacterium. We show that C. difficile reversibly differentiates into rough and smooth colony morphologies and that bacteria derived from the isolates display discrete motility behaviors. We identified an atypical phase-variable signal transduction system consisting of a histidine kinase and two response regulators, named herein colony morphology regulators RST (CmrRST), which mediates the switch in colony morphology and motility behaviors. The CmrRST-regulated surface motility is independent of flagella and type IV pili, suggesting a novel mechanism of cell migration in C. difficile. Microscopic analysis of cell and colony structure indicates that CmrRST promotes the formation of elongated bacteria arranged in bundled chains, which may contribute to bacterial migration on surfaces. In a hamster model of acute C. difficile disease, the CmrRST system is required for disease development. Furthermore, we provide evidence that CmrRST phase varies during infection, suggesting that the intestinal environment impacts the proportion of CmrRST-expressing C. difficile. Our findings indicate that C. difficile employs phase variation of the CmrRST signal transduction system to generate phenotypic heterogeneity during infection, with concomitant effects on bacterial physiology and pathogenesis. In many bacterial species, a genetically clonal population can generate phenotypic heterogeneity to ensure survival of a subpopulation in the face of sudden environmental stressors. This work shows that the intestinal pathogen Clostridioides difficile introduces heterogeneity into the population through the phase-variable expression of a signal transduction system, resulting in broad changes in physiology, motility, and virulence.
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Robinson JI, Weir WH, Crowley JR, Hink T, Reske KA, Kwon JH, Burnham CAD, Dubberke ER, Mucha PJ, Henderson JP. Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections. J Clin Invest 2019; 129:3792-3806. [PMID: 31403473 DOI: 10.1172/jci126905] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile infection (CDI) accounts for a substantial proportion of deaths attributable to antibiotic-resistant bacteria in the United States. Although C. difficile can be an asymptomatic colonizer, its pathogenic potential is most commonly manifested in patients with antibiotic-modified intestinal microbiomes. In a cohort of 186 hospitalized patients, we showed that host and microbe-associated shifts in fecal metabolomes had the potential to distinguish patients with CDI from those with non-C. difficile diarrhea and C. difficile colonization. Patients with CDI exhibited a chemical signature of Stickland amino acid fermentation that was distinct from those of uncolonized controls. This signature suggested that C. difficile preferentially catabolizes branched chain amino acids during CDI. Unexpectedly, we also identified a series of noncanonical, unsaturated bile acids that were depleted in patients with CDI. These bile acids may derive from an extended host-microbiome dehydroxylation network in uninfected patients. Bile acid composition and leucine fermentation defined a prototype metabolomic model with potential to distinguish clinical CDI from asymptomatic C. difficile colonization.
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Affiliation(s)
- John I Robinson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - William H Weir
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, and Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jan R Crowley
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A Reske
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennie H Kwon
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Erik R Dubberke
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Peter J Mucha
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, and Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jeffrey P Henderson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
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Muñoz M, Restrepo-Montoya D, Kumar N, Iraola G, Camargo M, Díaz-Arévalo D, Roa-Molina NS, Tellez MA, Herrera G, Ríos-Chaparro DI, Birchenall C, Pinilla D, Pardo-Oviedo JM, Rodríguez-Leguizamón G, Josa DF, Lawley TD, Patarroyo MA, Ramírez JD. Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia. Sci Rep 2019; 9:11293. [PMID: 31383872 PMCID: PMC6683185 DOI: 10.1038/s41598-019-47688-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/22/2019] [Indexed: 02/06/2023] Open
Abstract
Clostridium difficile, the causal agent of antibiotic-associated diarrhea, has a complex epidemiology poorly studied in Latin America. We performed a robust genomic and phenotypic profiling of 53 C. difficile clinical isolates established from diarrheal samples from either intrahospital (IH) or community (CO) populations in central Colombia. In vitro tests were conducted to evaluate the cytopathic effect, the minimum inhibitory concentration of ten antimicrobial agents, the sporulation efficiency and the colony forming ability. Eleven different sequence types (STs) were found, the majority present individually in each sample, however in three samples two different STs were isolated. Interestingly, CO patients were infected with STs associated with hypervirulent strains (ST-1 in Clade-2). Three coexistence events (two STs simultaneously detected in the same sample) were observed always involving ST-8 from Clade-1. A total of 2,502 genes were present in 99% of the isolates with 95% of identity or more, it represents a core genome of 28.6% of the 8,735 total genes identified in the set of genomes. A high cytopathic effect was observed for the isolates positive for the two main toxins but negative for binary toxin (TcdA+/TcdB+/CDT- toxin production type), found only in Clade-1. Molecular markers conferring resistance to fluoroquinolones (cdeA and gyrA) and to sulfonamides (folP) were the most frequent in the analyzed genomes. In addition, 15 other markers were found mostly in Clade-2 isolates. These results highlight the regional differences that C. difficile isolates display, being in this case the CO isolates the ones having a greater number of accessory genes and virulence-associated factors.
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Affiliation(s)
- Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Posgrado Interfacultades Doctorado en Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniel Restrepo-Montoya
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Genomics and Bioinformatics Department, North Dakota State University, Fargo, North Dakota, USA
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur Montevideo, Montevideo, Uruguay
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile
| | - Milena Camargo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Diana Díaz-Arévalo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Faculty of Animal Sciences, Universidad de Ciencias Aplicadas y Ambientales (UDCA), Bogotá, Colombia
- Hygea group, Faculty of Health Sciences, Universidad de Boyacá, Tunja, Colombia
| | - Nelly S Roa-Molina
- Centro de Investigaciones Odontológicas, Facultad de Odontología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Mayra A Tellez
- Centro de Investigaciones Odontológicas, Facultad de Odontología, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Giovanny Herrera
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- PhD Programme in Biomedical and Biological Sciences, Faculty of Natural Sciences and Mathematics/School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Dora I Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
| | - Claudia Birchenall
- Hospital Universitario Mayor - Méderi, Universidad del Rosario, Bogotá, Colombia
| | - Darío Pinilla
- Hospital Universitario Mayor - Méderi, Universidad del Rosario, Bogotá, Colombia
| | - Juan M Pardo-Oviedo
- Hospital Universitario Mayor - Méderi, Universidad del Rosario, Bogotá, Colombia
| | | | | | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia.
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Evaluation of growth and sporulation of a non-toxigenic strain of Clostridioides difficile (Z31) and its shelf viability. Braz J Microbiol 2019; 50:263-269. [PMID: 30637658 DOI: 10.1007/s42770-018-0023-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 08/07/2018] [Indexed: 10/27/2022] Open
Abstract
The oral administration of non-toxigenic strains of Clostridioides difficile (NTCD) is currently showing promising results for the prevention of Clostridioides difficile infection (CDI) in humans and animals, and is being considered as a possible commercial product to be used in the near future. The aim of this work was to evaluate five culture media for the growth and sporulation of one NTCD (Z31) and evaluate the viability of a lyophilized spore solution of NTCD Z31 stored at 4 °C or at 25 °C for 2 years. Reinforced clostridial medium (RCM) and brain heart infusion broth (BHI) provided the highest production of NTCD Z31 spores. In the first 6 months of the storage of the lyophilized solution, a reduction in spore count of approximately 0.3 Log10 CFU/mL was observed; however, no further significant reduction in spore count was observed up to 24 months. No difference in spore concentration was found between the two storage temperatures from 6 to 24 months of storage. The present work showed BHI and RCM to be the best choices for the growth and sporulation of NTCD Z31 and suggested that the spores of NTCD Z31 are stable for up to 2 years under both temperature conditions.
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Ünal CM, Berges M, Smit N, Schiene-Fischer C, Priebe C, Strowig T, Jahn D, Steinert M. PrsA2 (CD630_35000) of Clostridioides difficile Is an Active Parvulin-Type PPIase and a Virulence Modulator. Front Microbiol 2018; 9:2913. [PMID: 30564207 PMCID: PMC6288519 DOI: 10.3389/fmicb.2018.02913] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/13/2018] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is the main cause for nosocomial antibiotic associated diarrhea and has become a major burden for the health care systems of industrial countries. Its main virulence factors, the small GTPase glycosylating toxins TcdA and TcdB, are extensively studied. In contrast, the contribution of other factors to development and progression of C. difficile infection (CDI) are only insufficiently understood. Many bacterial peptidyl-prolyl-cis/trans-isomerases (PPIases) have been described in the context of virulence. Among them are the parvulin-type PrsA-like PPIases of Gram-positive bacteria. On this basis, we identified CD630_35000 as the PrsA2 homolog in C. difficile and conducted its enzymatic and phenotypic characterization in order to assess its involvement during C. difficile infection. For this purpose, wild type CdPrsA2 and mutant variants carrying amino acid exchanges mainly in the PPIase domain were recombinantly produced. Recombinant CdPrsA2 showed PPIase activity toward the substrate peptide Ala-Xaa-Pro-Phe with a preference for positively charged amino acids preceding the proline residue. Mutation of conserved residues in its active site pocket impaired the enzymatic activity. A PrsA2 deficient mutant was generated in the C. difficile 630Δerm background using the ClosTron technology. Inactivation of prsA2 resulted in a reduced germination rate in response to taurocholic acid, and in a slight increase in resistance to the secondary bile acids LCA and DCA. Interestingly, in the absence of PrsA2 colonization of mice by C. difficile 630 was significantly reduced. We concluded that CdPrsA2 is an active PPIase that acts as a virulence modulator by influencing crucial processes like sporulation, germination and bile acid resistance resulting in attenuated mice colonization.
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Affiliation(s)
- Can Murat Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Türk-Alman Üniversitesi, Moleküler Biyoteknoloji Bölümü, Istanbul, Turkey
| | - Mareike Berges
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nathiana Smit
- Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Cordelia Schiene-Fischer
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Christina Priebe
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Till Strowig
- Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany
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Abstract
Bacillus and Clostridium spores are known to be highly resistant to killing, persisting on environmental and human body surfaces for long periods of time. In favorable environments, these spores may germinate and cause human diseases. It is thus important to identify agents that can be used on both environmental and human skin and mucosal surfaces and that are effective in killing spores. We previously showed that the fatty acid monoester glycerol monolaurate (GML) kills stationary-phase cultures of Bacillus anthracis. Since such cultures are likely to contain spores, it is possible that GML and a human-use-approved GML nonaqueous gel would kill Bacillus and Clostridium spores. The significance of our studies is that we have identified GML, and, to a greater extent, GML solubilized in a nonaqueous gel, as effective in killing spores from both bacterial genera. Glycerol monolaurate is a broadly antimicrobial fatty acid monoester, killing bacteria, fungi, and enveloped viruses. The compound kills stationary-phase cultures of Bacillus anthracis, suggesting that the molecule may kill spores. In this study, we examined the ability of glycerol monolaurate alone or solubilized in a nonaqueous gel to kill vegetative cells and spores of aerobic B. anthracis, B. subtilis, and B. cereus and anaerobic Clostridium perfringens and Clostridium (Clostridioides) difficile. Glycerol monolaurate alone was bactericidal for all five organisms tested. Glycerol monolaurate alone was effective in killing spores. When solubilized in a nonaqueous gel, the glycerol monolaurate gel was bactericidal for all spores tested. The data suggest that glycerol monolaurate nonaqueous gel could be effective in decontaminating environmental and body surfaces, such as skin. IMPORTANCEBacillus and Clostridium spores are known to be highly resistant to killing, persisting on environmental and human body surfaces for long periods of time. In favorable environments, these spores may germinate and cause human diseases. It is thus important to identify agents that can be used on both environmental and human skin and mucosal surfaces and that are effective in killing spores. We previously showed that the fatty acid monoester glycerol monolaurate (GML) kills stationary-phase cultures of Bacillus anthracis. Since such cultures are likely to contain spores, it is possible that GML and a human-use-approved GML nonaqueous gel would kill Bacillus and Clostridium spores. The significance of our studies is that we have identified GML, and, to a greater extent, GML solubilized in a nonaqueous gel, as effective in killing spores from both bacterial genera.
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Ransom EM, Kaus GM, Tran PM, Ellermeier CD, Weiss DS. Multiple factors contribute to bimodal toxin gene expression in Clostridioides (Clostridium) difficile. Mol Microbiol 2018; 110:533-549. [PMID: 30125399 PMCID: PMC6446242 DOI: 10.1111/mmi.14107] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/10/2018] [Accepted: 08/11/2018] [Indexed: 12/14/2022]
Abstract
Clostridioides (formerly Clostridium) difficile produces two major toxins, TcdA and TcdB, upon entry into stationary phase. Transcription of tcdA and tcdB requires the specialized sigma factor, σTcdR , which also directs RNA Polymerase to transcribe tcdR itself. We fused a gene for a red fluorescent protein to the tcdA promoter to study toxin gene expression at the level of individual C. difficile cells. Surprisingly, only a subset of cells became red fluorescent upon entry into stationary phase. Breaking the positive feedback loop that controls σTcdR production by engineering cells to express tcdR from a tetracycline-inducible promoter resulted in uniform fluorescence across the population. Experiments with two regulators of tcdR expression, σD and CodY, revealed neither is required for bimodal toxin gene expression. However, σD biased cells toward the Toxin-ON state, while CodY biased cells toward the Toxin-OFF state. Finally, toxin gene expression was observed in sporulating cells. We conclude that (i) toxin production is regulated by a bistable switch governed by σTcdR , which only accumulates to high enough levels to trigger toxin gene expression in a subset of cells, and (ii) toxin production and sporulation are not mutually exclusive developmental programs.
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Affiliation(s)
- Eric M. Ransom
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Gabriela M. Kaus
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Phuong M. Tran
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Craig D. Ellermeier
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242
| | - David S. Weiss
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242
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46
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Abstract
Clostridium difficile is an anaerobic spore-forming human pathogen that is the leading cause of nosocomial infectious diarrhea worldwide. Germination of infectious spores is the first step in the development of a C. difficile infection (CDI) after ingestion and passage through the stomach. This study investigates the specific conditions that facilitate C. difficile spore germination, including the following: location within the gastrointestinal (GI) tract, pH, temperature, and germinant concentration. The germinants that have been identified in culture include combinations of bile salts and amino acids or bile salts and calcium, but in vitro, these function at concentrations that far exceed normal physiological ranges normally found in the mammalian GI tract. In this work, we describe and quantify a previously unreported synergy observed when bile salts, calcium, and amino acids are added together. These germinant cocktails improve germination efficiency by decreasing the required concentrations of germinants to physiologically relevant levels. Combinations of multiple germinant types are also able to overcome the effects of inhibitory bile salts. In addition, we propose that the acidic conditions within the GI tract regulate C. difficile spore germination and could provide a biological explanation for why patients taking proton pump inhibitors are associated with increased risk of developing a CDI. Clostridium difficile is a Gram-positive obligate anaerobe that forms spores in order to survive for long periods in the unfavorable environment outside a host. C. difficile is the leading cause of nosocomial infectious diarrhea worldwide. C. difficile infection (CDI) arises after a patient treated with broad-spectrum antibiotics ingests infectious spores. The first step in C. difficile pathogenesis is the metabolic reactivation of dormant spores within the gastrointestinal (GI) tract through a process known as germination. In this work, we aim to elucidate the specific conditions and the location within the GI tract that facilitate this process. Our data suggest that C. difficile germination occurs through a two-step biochemical process that is regulated by pH and bile salts, amino acids, and calcium present within the GI tract. Maximal germination occurs at a pH ranging from 6.5 to 8.5 in the terminal small intestine prior to bile salt and calcium reabsorption by the host. Germination can be initiated by lower concentrations of germinants when spores are incubated with a combination of bile salts, calcium, and amino acids, and this synergy is dependent on the availability of calcium. The synergy described here allows germination to proceed in the presence of inhibitory bile salts and at physiological concentrations of germinants, effectively decreasing the concentrations of nutrients required to initiate an essential step of pathogenesis. IMPORTANCEClostridium difficile is an anaerobic spore-forming human pathogen that is the leading cause of nosocomial infectious diarrhea worldwide. Germination of infectious spores is the first step in the development of a C. difficile infection (CDI) after ingestion and passage through the stomach. This study investigates the specific conditions that facilitate C. difficile spore germination, including the following: location within the gastrointestinal (GI) tract, pH, temperature, and germinant concentration. The germinants that have been identified in culture include combinations of bile salts and amino acids or bile salts and calcium, but in vitro, these function at concentrations that far exceed normal physiological ranges normally found in the mammalian GI tract. In this work, we describe and quantify a previously unreported synergy observed when bile salts, calcium, and amino acids are added together. These germinant cocktails improve germination efficiency by decreasing the required concentrations of germinants to physiologically relevant levels. Combinations of multiple germinant types are also able to overcome the effects of inhibitory bile salts. In addition, we propose that the acidic conditions within the GI tract regulate C. difficile spore germination and could provide a biological explanation for why patients taking proton pump inhibitors are associated with increased risk of developing a CDI.
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Woods EC, Edwards AN, Childress KO, Jones JB, McBride SM. The C. difficile clnRAB operon initiates adaptations to the host environment in response to LL-37. PLoS Pathog 2018; 14:e1007153. [PMID: 30125334 PMCID: PMC6117091 DOI: 10.1371/journal.ppat.1007153] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/30/2018] [Accepted: 07/16/2018] [Indexed: 01/05/2023] Open
Abstract
To cause disease, Clostridioides (Clostridium) difficile must resist killing by innate immune effectors in the intestine, including the host antimicrobial peptide, cathelicidin (LL-37). The mechanisms that enable C. difficile to adapt to the intestine in the presence of antimicrobial peptides are unknown. Expression analyses revealed an operon, CD630_16170-CD630_16190 (clnRAB), which is highly induced by LL-37 and is not expressed in response to other cell-surface active antimicrobials. This operon encodes a predicted transcriptional regulator (ClnR) and an ABC transporter system (ClnAB), all of which are required for function. Analyses of a clnR mutant indicate that ClnR is a pleiotropic regulator that directly binds to LL-37 and controls expression of numerous genes, including many involved in metabolism, cellular transport, signaling, gene regulation, and pathogenesis. The data suggest that ClnRAB is a novel regulatory mechanism that senses LL-37 as a host signal and regulates gene expression to adapt to the host intestinal environment during infection.
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Affiliation(s)
- Emily C. Woods
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Adrianne N. Edwards
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Kevin O. Childress
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Joshua B. Jones
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Shonna M. McBride
- Department of Microbiology and Immunology, and Emory University Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States of America
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Type IV Pili Promote Clostridium difficile Adherence and Persistence in a Mouse Model of Infection. Infect Immun 2018; 86:IAI.00943-17. [PMID: 29483294 DOI: 10.1128/iai.00943-17] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/21/2018] [Indexed: 12/16/2022] Open
Abstract
Cyclic diguanylate (c-di-GMP) is a second messenger that regulates the transition from motile to sessile lifestyles in numerous bacteria and controls virulence factor production in a variety of pathogens. In Clostridium difficile, c-di-GMP negatively regulates flagellum biosynthesis and swimming motility and promotes the production of type IV pili (TFP), biofilm formation, and surface motility in vitro Flagella have been identified as colonization factors in C. difficile, but the role of TFP in adherence to host cells and in colonization of the mammalian gut is unknown. Here we show that c-di-GMP promotes adherence to epithelial cells in vitro, which can be partly attributed to the loss of flagella. Using TFP-null mutants, we demonstrate that adherence to epithelial cells is partially mediated by TFP and that this TFP-mediated adherence requires c-di-GMP regulation. In a mouse model of colonization, the TFP-null mutants initially colonized the intestine as well as the parental strain but were cleared more quickly. Moreover, compared to the parent strain, C. difficile strains lacking TFP were particularly deficient in association with the cecal mucosa. Together these data indicate that TFP and their positive regulation by c-di-GMP promote attachment of C. difficile to the intestinal epithelium and contribute to persistence of C. difficile in the host intestine.
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Nawrocki KL, Wetzel D, Jones JB, Woods EC, McBride SM. Ethanolamine is a valuable nutrient source that impacts Clostridium difficile pathogenesis. Environ Microbiol 2018; 20:1419-1435. [PMID: 29349925 PMCID: PMC5903940 DOI: 10.1111/1462-2920.14048] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 01/03/2018] [Accepted: 01/14/2018] [Indexed: 12/12/2022]
Abstract
Clostridium (Clostridioides) difficile is a gastrointestinal pathogen that colonizes the intestinal tract of mammals and can cause severe diarrheal disease. Although C. difficile growth is confined to the intestinal tract, our understanding of the specific metabolites and host factors that are important for the growth of the bacterium is limited. In other enteric pathogens, the membrane-derived metabolite, ethanolamine (EA), is utilized as a nutrient source and can function as a signal to initiate the production of virulence factors. In this study, we investigated the effects of ethanolamine and the role of the predicted ethanolamine gene cluster (CD1907-CD1925) on C. difficile growth. Using targeted mutagenesis, we disrupted genes within the eut cluster and assessed their roles in ethanolamine utilization, and the impact of eut disruption on the outcome of infection in a hamster model of disease. Our results indicate that the eut gene cluster is required for the growth of C. difficile on ethanolamine as a primary nutrient source. Further, the inability to utilize ethanolamine resulted in greater virulence and a shorter time to morbidity in the animal model. Overall, these data suggest that ethanolamine is an important nutrient source within the host and that, in contrast to other intestinal pathogens, the metabolism of ethanolamine by C. difficile can delay the onset of disease.
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Affiliation(s)
- Kathryn L. Nawrocki
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Daniela Wetzel
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshua B. Jones
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Emily C. Woods
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, and Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA
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Bishop AH. Potentiating Effect of Mandelate and Lactate on Chemically Induced Germination in Members of Bacillus cereus Sensu Lato. Appl Environ Microbiol 2017; 83:e01722-17. [PMID: 28970226 PMCID: PMC5717211 DOI: 10.1128/aem.01722-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/24/2017] [Indexed: 11/20/2022] Open
Abstract
Endospores of the genus Bacillus can be triggered to germinate by a limited number of chemicals. Mandelate had powerful additive effects on the levels and rates of germination produced in non-heat-shocked spores of Bacillus anthracis strain Sterne, Bacillus cereus, and Bacillus thuringiensis when combined with l-alanine and inosine. Mandelate had no germinant effect on its own but was active with these germinants in a dose-dependent manner at concentrations higher than 0.5 mM. The maximum rate and extent of germination were produced in B. anthracis by 100 mM l-alanine with 10 mM inosine; this was equaled by just 25% of these germinants when supplemented with 10 mM mandelate. Half the maximal germination rate was produced by 40% of the optimum germinant concentrations or 15% of them when supplemented with 0.8 mM mandelate. Germination rates in B. thuringiensis were highest around neutrality, but the potentiating effect of mandelate was maintained over a wider pH range than was germination with l-alanine and inosine alone. For all species, lactate also promoted germination in the presence of l-alanine and inosine; this was further increased by mandelate. Ammonium ions also enhanced l-alanine- and inosine-induced germination but only when mandelate was present. In spite of the structural similarities, mandelate did not compete with phenylalanine as a germinant. Mandelate appeared to bind to spores while enhancing germination. There was no effect when mandelate was used in conjunction with nonnutrient germinants. No effect was produced with spores of Bacillus subtilis, Clostridium sporogenes, or C. difficileIMPORTANCE The number of chemicals that can induce germination in the species related to Bacillus cereus has been defined for many years, and they conform to specific chemical types. Although not a germinant itself, mandelate has a structure that is different from these germination-active compounds, and its addition to this list represents a significant discovery in the fundamental biology of spore germination. This novel activity may also have important applied relevance given the impact of spores of B. cereus in foodborne disease and B. anthracis as a threat agent. The destruction of spores of B. anthracis, for example, particularly over large outdoor areas, poses significant scientific and logistical problems. The addition of mandelate and lactate to the established mixtures of l-alanine and inosine would decrease the amount of the established germinants required and increase the speed and level of germination achieved. The large-scale application of "germinate to decontaminate" strategy may thus become more practicable.
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Affiliation(s)
- Alistair H Bishop
- School of Biological and Marine Sciences, University of Plymouth, Devon, United Kingdom
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